What's in your next-generation sequence data? An exploration of unmapped DNA and RNA sequence reads from the bovine reference individual.

BackgroundNext-generation sequencing projects commonly commence by aligning reads to a reference genome assembly. While improvements in alignment algorithms and computational hardware have greatly enhanced the efficiency and accuracy of alignments, a significant percentage of reads often remain unmapped.ResultsWe generated de novo assemblies of unmapped reads from the DNA and RNA sequencing of the Bos taurus reference individual and identified the closest matching sequence to each contig by alignment to the NCBI non-redundant nucleotide database using BLAST. As expected, many of these contigs represent vertebrate sequence that is absent, incomplete, or misassembled in the UMD3.1 reference assembly. However, numerous additional contigs represent invertebrate species. Most prominent were several species of Spirurid nematodes and a blood-borne parasite, Babesia bigemina. These species are either not present in the US or are not known to infect taurine cattle and the reference animal appears to have been host to unsequenced sister species.ConclusionsWe demonstrate the importance of exploring unmapped reads to ascertain sequences that are either absent or misassembled in the reference assembly and for detecting sequences indicative of parasitic or commensal organisms

Osteosarcoma Phenotype Is Inhibited by 3,4-Methylenedioxy-β-nitrostyrene

β-nitrostyrene compounds, such as 3,4-methylenedioxy-β-nitrostyrene (MNS), inhibit growth and induce apoptosis in tumor cells, but no reports have investigated their role in osteosarcoma. In this study, human osteosarcoma cell families with cell lines of varying tumorigenic and metastatic potential were utilized. Scrape motility assays, colony formation assays, and colony survival assays were performed with osteosarcoma cell lines, both in the presence and absence of MNS. Effects of MNS on human osteoblasts and airway epithelial cells were assessed in monolayer cultures. MNS decreased metastatic cell line motility by 72–76% and colony formation by 95–100%. MNS consistently disrupted preformed colonies in a time-dependent and dose-dependent manner. MNS had similar effects on human osteoblasts but little effect on airway epithelial cells. An inactive analog of MNS had no detectable effects, demonstrating specificity. MNS decreases motility and colony formation of osteosarcoma cells and disrupts preformed cell colonies, while producing little effect on pulmonary epithelial cells

Life Cycle Water Consumption and Water Resource Assessment for Utility-Scale Geothermal Systems: An In-Depth Analysis of Historical and Forthcoming EGS Projects

This report is the third in a series of reports sponsored by the U.S. Department of Energy Geothermal Technologies Program in which a range of water-related issues surrounding geothermal power production are evaluated. The first report made an initial attempt at quantifying the life cycle fresh water requirements of geothermal power-generating systems and explored operational and environmental concerns related to the geochemical composition of geothermal fluids. The initial analysis of life cycle fresh water consumption of geothermal power-generating systems identified that operational water requirements consumed the vast majority of water across the life cycle. However, it relied upon limited operational water consumption data and did not account for belowground operational losses for enhanced geothermal systems (EGSs). A second report presented an initial assessment of fresh water demand for future growth in utility-scale geothermal power generation. The current analysis builds upon this work to improve life cycle fresh water consumption estimates and incorporates regional water availability into the resource assessment to improve the identification of areas where future growth in geothermal electricity generation may encounter water challenges. This report is divided into nine chapters. Chapter 1 gives the background of the project and its purpose, which is to assess the water consumption of geothermal technologies and identify areas where water availability may present a challenge to utility-scale geothermal development. Water consumption refers to the water that is withdrawn from a resource such as a river, lake, or nongeothermal aquifer that is not returned to that resource. The geothermal electricity generation technologies evaluated in this study include conventional hydrothermal flash and binary systems, as well as EGSs that rely on engineering a productive reservoir where heat exists, but where water availability or permeability may be limited. Chapter 2 describes the approach and methods for this work and identifies the four power plant scenarios evaluated: a 20-MW EGS binary plant, a 50-MW EGS binary plant, a 10-MW hydrothermal binary plant, and a 50-MW hydrothermal flash plant. The methods focus on (1) the collection of data to improve estimation of EGS stimulation volumes, aboveground operational consumption for all geothermal technologies, and belowground operational consumption for EGS; and (2) the mapping of the geothermal and water resources of the western United States to assist in the identification of potential water challenges to geothermal growth. Chapters 3 and 4 present the water requirements for the power plant life cycle. Chapter 3 presents the results of the current data collection effort, and Chapter 4 presents the normalized volume of fresh water consumed at each life cycle stage per lifetime energy output for the power plant scenarios evaluated. Over the life cycle of a geothermal power plant, from construction through 30 years of operation, the majority of water is consumed by plant operations. For the EGS binary scenarios, where dry cooling was assumed, belowground operational water loss is the greatest contributor depending upon the physical and operational conditions of the reservoir. Total life cycle water consumption requirements for air-cooled EGS binary scenarios vary between 0.22 and 1.85 gal/kWh, depending upon the extent of belowground operational water consumption. The air-cooled hydrothermal binary and flash plants experience far less fresh water consumption over the life cycle, at 0.04 gal/kWh. Fresh water requirements associated with air- cooled binary operations are primarily from aboveground water needs, including dust control, maintenance, and domestic use. Although wet-cooled hydrothermal flash systems require water for cooling, these plants generally rely upon the geofluid, fluid from the geothermal reservoir, which typically has high salinity and total dissolved solids concentration and is much warmer than normal groundwater sources, for their cooling water needs; thus, while there is considerable geofluid loss at 2.7 gal/kWh, fresh water consumption during operations is similar to that of aircooled binary systems. Chapter 5 presents the assessment of water demand for future growth in deployment of utility-scale geothermal power generation. The approach combines the life cycle analysis of geothermal water consumption with a geothermal supply curve according to resource type, levelized cost of electricity (LCOE), and potential growth scenarios. A total of 17 growth scenarios were evaluated. In general, the scenarios that assumed lower costs for EGSs as a result of learning and technological improvements resulted in greater geothermal potential, but also significantly greater water demand due to the higher water consumption by EGSs. It was shown, however, that this effect could be largely mitigated if nonpotable water sources were used for belowground operational water demands. The geographical areas that showed the highest water demand for most growth scenarios were southern and northern California, as well as most of Nevada. In addition to water demand by geothermal power production, Chapter 5 includes data on water availability for geothermal development areas. A qualitative analysis is included that identifies some of the basins where the limited availability of water is most likely to affect the development of geothermal resources. The data indicate that water availability is fairly limited, especially under drought conditions, in most of the areas with significant near- and medium-term geothermal potential. Southern California was found to have the greatest potential for water-related challenges with its combination of high geothermal potential and limited water availability. The results of this work are summarized in Chapter 6. Overall, this work highlights the importance of utilizing dry cooling systems for binary and EGS systems and minimizing fresh water consumption throughout the life cycle of geothermal power development. The large resource base for EGSs represents a major opportunity for the geothermal industry; however, depending upon geology, these systems can require large quantities of makeup water due to belowground reservoir losses. Identifying potential sources of compatible degraded or low-quality water for use for makeup injection for EGS and flash systems represents an important opportunity to reduce the impacts of geothermal development on fresh water resources. The importance of identifying alternative water sources for geothermal systems is heightened by the fact that a large fraction of the geothermal resource is located in areas already experiencing water stress. Chapter 7 is a glossary of the technical terms used in the report, and Chapters 8 and 9 provide references and a bibliography, respectively

Modular ‘Click-in-Emulsion’ Bone-Targeted Nanogels

A new class of nanogel demonstrates modular biodistribution and affinity for bone. Nanogels, ~70 nm in diameter and synthesized via an astoichiometric click-chemistry in-emulsion method, controllably display residual, free clickable functional groups. Functionalization with a bisphosphonate ligand results in significant binding to bone on the inner walls of marrow cavities, liver avoidance, and anti-osteoporotic effects.National Institutes of Health (U.S.) (RO1 DE016516)National Institutes of Health (U.S.) (R01 EB000244)Damon Runyon Cancer Research Foundation (DFS-#2050-10

Five decades of radioglaciology

Radar sounding is a powerful geophysical approach for characterizing the subsurface conditions of terrestrial and planetary ice masses at local to global scales. As a result, a wide array of orbital, airborne, ground-based, and in situ instruments, platforms and data analysis approaches for radioglaciology have been developed, applied or proposed. Terrestrially, airborne radar sounding has been used in glaciology to observe ice thickness, basal topography and englacial layers for five decades. More recently, radar sounding data have also been exploited to estimate the extent and configuration of subglacial water, the geometry of subglacial bedforms and the subglacial and englacial thermal states of ice sheets. Planetary radar sounders have observed, or are planned to observe, the subsurfaces and near-surfaces of Mars, Earth's Moon, comets and the icy moons of Jupiter. In this review paper, and the thematic issue of the Annals of Glaciology on ‘Five decades of radioglaciology’ to which it belongs, we present recent advances in the fields of radar systems, missions, signal processing, data analysis, modeling and scientific interpretation. Our review presents progress in these fields since the last radio-glaciological Annals of Glaciology issue of 2014, the context of their history and future prospects

Epidural Hematoma Following Cervical Spine Surgery.

STUDY DESIGN: A multicentered retrospective case series. OBJECTIVE: To determine the incidence and circumstances surrounding the development of a symptomatic postoperative epidural hematoma in the cervical spine. METHODS: Patients who underwent cervical spine surgery between January 1, 2005, and December 31, 2011, at 23 institutions were reviewed, and all patients who developed an epidural hematoma were identified. RESULTS: A total of 16 582 cervical spine surgeries were identified, and 15 patients developed a postoperative epidural hematoma, for a total incidence of 0.090%. Substantial variation between institutions was noted, with 11 sites reporting no epidural hematomas, and 1 site reporting an incidence of 0.76%. All patients initially presented with a neurologic deficit. Nine patients had complete resolution of the neurologic deficit after hematoma evacuation; however 2 of the 3 patients (66%) who had a delay in the diagnosis of the epidural hematoma had residual neurologic deficits compared to only 4 of the 12 patients (33%) who had no delay in the diagnosis or treatment (P = .53). Additionally, the patients who experienced a postoperative epidural hematoma did not experience any significant improvement in health-related quality-of-life metrics as a result of the index procedure at final follow-up evaluation. CONCLUSION: This is the largest series to date to analyze the incidence of an epidural hematoma following cervical spine surgery, and this study suggest that an epidural hematoma occurs in approximately 1 out of 1000 cervical spine surgeries. Prompt diagnosis and treatment may improve the chance of making a complete neurologic recovery, but patients who develop this complication do not show improvements in the health-related quality-of-life measurements

Third Way Environmentalism

This paper is explaining the important design phases of dimensioning an unmanned conventional aircraft from scratch and will also design one according to a few chosen requirements. The design phases discussed will be all from wing dimensioning to stability and spin recovery, aircraft performance requirements and how to select a motor which overcomes these. As well as the optimal rate of climb for improved efficiency is discussed. In the end an aircraft which manages the set requirements and is stable in pitch managing spin recovery with no problem will have been dimensioned